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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ), 'gf_id' => 'HOM05D001198', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001198' ), 'data_identifier' => 'HOM05D001198', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001198', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '522', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p08100' => 'bna', 'A03p42450' => 'bna', 'A05p26980' => 'bna', 'A07p08410' => 'bna', 'A09p07470' => 'bna', 'Aa31LG11G1580' => 'aar', 'Aa31LG8G8360' => 'aar', 'Aa31LG9G3110' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.1262' => 'aag', 'Actinidia08315' => 'ach', 'Actinidia08907' => 'ach', 'Actinidia09393' => 'ach', 'Actinidia12505' => 'ach', 'Actinidia20321' => 'ach', 'Actinidia24266' => 'ach', 'Actinidia32075' => 'ach', 'Actinidia36841' => 'ach', 'Ah.02g125660' => 'amhyb', 'Ah.04g166080' => 'amhyb', 'Ah.11g046880' => 'amhyb', 'AL2G19190' => 'aly', 'AL3G35870' => 'aly', 'AL8G34000' => 'aly', 'AL8G38690' => 'aly', 'Aqoxy2G03507' => 'aox', 'Aqoxy5G03138' => 'aox', 'Aqoxy6G02963' => 'aox', 'Aqoxy7G00333' => 'aox', 'Aqoxy7G01653' => 'aox', 'Aqoxy7G02127' => 'aox', 'Aqoxy7G02128' => 'aox', 'arahy.Tifrunner.gnm1.ann1.2PHP7C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.45ZRCR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.55LQUQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.837L0J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8Z2PYB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.958XRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9BJ9H4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A9YW0Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AB69EK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJT3C2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GW9QEL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JJ1YCM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.L4DPYZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MHD2AA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MR39VQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q5EMMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X3UY05' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YVA47Q' => 'arhy', 'AT1G64810' => 'ath', 'AT3G21740' => 'ath', 'AT5G57930' => 'ath', 'AT5G61930' => 'ath', 'ATR0006G049' => 'atr', 'ATR0580G368' => 'atr', 'ATR0598G188' => 'atr', 'ATR0680G330' => 'atr', 'Atru.BG.158.p' => 'acertr', 'Atru.chr1.1683' => 'acertr', 'Atru.chr5.1944' => 'acertr', 'Atru.chr6.1372' => 'acertr', 'Atru.chr6.1914' => 'acertr', 'Atru.chr6.3158' => 'acertr', 'Atru.chr7.36' => 'acertr', 'AUR62003975' => 'cqu', 'AUR62009536' => 'cqu', 'AUR62011455' => 'cqu', 'AUR62015865' => 'cqu', 'AUR62016602' => 'cqu', 'AUR62026128' => 'cqu', 'AUR62040270' => 'cqu', 'AUR62041700' => 'cqu', 'BcaB01g02073' => 'bca', 'BcaB05g22387' => 'bca', 'BcaB06g26280' => 'bca', 'BcaB06g26560' => 'bca', 'BcaC01g02449' => 'bca', 'BcaC01g03485' => 'bca', 'BcaC04g23433' => 'bca', 'BcaC05g28133' => 'bca', 'BcaC06g35596' => 'bca', 'BcaNung01416' => 'bca', 'BolC2t07493H' => 'bol', 'BolC3t18769H' => 'bol', 'BolC5t32900H' => 'bol', 'BolC7t41807H' => 'bol', 'BolC9t53748H' => 'bol', 'BraA02t05883Z' => 'bra', 'BraA03t13398Z' => 'bra', 'BraA03t13399Z' => 'bra', 'BraA05t21580Z' => 'bra', 'BraA07t28626Z' => 'bra', 'BraA09t36401Z' => 'bra', 'C02p13750' => 'bna', 'C03p51970' => 'bna', 'C03p65170' => 'bna', 'C05p00670' => 'bna', 'C05p41630' => 'bna', 'C07p13120' => 'bna', 'C09p08380' => 'bna', 'CAN.G1126.29' => 'can', 'CAN.G160.65' => 'can', 'CAN.G397.8' => 'can', 'CAN.G981.41' => 'can', 'CANSAT11G1434' => 'cansat', 'CANSAT35G1499' => 'cansat', 'CARHR056230' => 'chi', 'CARHR097680' => 'chi', 'CARHR271710' => 'chi', 'CARHR275690' => 'chi', 'Carub.0002s1006' => 'cru', 'Carub.0003s2178' => 'cru', 'Carub.0008s1846' => 'cru', 'Carub.0008s2261' => 'cru', 'Carub.0095s0001' => 'cru', 'Ca_01591_v3' => 'car', 'Ca_01978_v3' => 'car', 'Ca_02137_v3' => 'car', 'Ca_05638_v3' => 'car', 'Ca_25390_v3' => 'car', 'Ca_29774_v3' => 'car', 'CBR_g23288' => 'cbr', 'Cc01_g04250' => 'ccan', 'Cc03_g00090' => 'ccan', 'Cc06_g14880' => 'ccan', 'Cc10_g03190' => 'ccan', 'CDE01G0379' => 'cde', 'CDE02G4576' => 'cde', 'CDE05G1213' => 'cde', 'CDE06G0026' => 'cde', 'CDE06G0057' => 'cde', 'CDE12G0856' => 'cde', 'Cfa007292' => 'cfa', 'Cfa014431' => 'cfa', 'Cfa014959' => 'cfa', 'Cfa018708' => 'cfa', 'Cfa020821' => 'cfa', 'Ciclev10008334m.g' => 'ccl', 'Ciclev10015251m.g' => 'ccl', 'Ciclev10015921m.g' => 'ccl', 'Ciclev10028534m.g' => 'ccl', 'Ciclev10031524m.g' => 'ccl', 'CiPaw.03G187400' => 'cil', 'CiPaw.07G107700' => 'cil', 'CiPaw.10G084600' => 'cil', 'CiPaw.12G027900' => 'cil', 'CiPaw.16G109300' => 'cil', 'CiPaw.16G110400' => 'cil', 'ClCG02G008480' => 'cla', 'ClCG06G012440' => 'cla', 'ClCG06G018360' => 'cla', 'ClCG09G005900' => 'cla', 'ClCG11G016740' => 'cla', 'COL.COLO4_15725' => 'col', 'COL.COLO4_17525' => 'col', 'COL.COLO4_18814' => 'col', 'COL.COLO4_32433' => 'col', 'Cpa.g.sc136.43' => 'cpa', 'Cpa.g.sc136.69' => 'cpa', 'Cpa.g.sc136.70' => 'cpa', 'Cpa.g.sc20.51' => 'cpa', 'Cpa.g.sc27.189' => 'cpa', 'Cpa.g.sc8.226' => 'cpa', 'CsaV3_1G029000' => 'csa', 'CsaV3_2G035140' => 'csa', 'CsaV3_4G032240' => 'csa', 'CsaV3_5G015000' => 'csa', 'CsaV3_7G029250' => 'csa', 'CSS0007414' => 'camsi', 'CSS0020945' => 'camsi', 'CSS0024979' => 'camsi', 'CSS0032081' => 'camsi', 'CSS0036633' => 'camsi', 'CSS0046509' => 'camsi', 'DCAR_003527' => 'dca', 'DCAR_008758' => 'dca', 'DCAR_019398' => 'dca', 'DCAR_023062' => 'dca', 'DCAR_025648' => 'dca', 'Dinv04530' => 'din', 'Dinv04532' => 'din', 'Dinv07278' => 'din', 'Dinv08267' => 'din', 'Dinv20246' => 'din', 'Dinv25974' => 'din', 'Dinv42849' => 'din', 'Dinv43251' => 'din', 'Duzib138G0219' => 'dzi', 'Duzib168G0751' => 'dzi', 'Duzib205G0997' => 'dzi', 'Duzib213G0991' => 'dzi', 'ECA232G0460' => 'eca', 'ECA233G0171' => 'eca', 'ECA248G2689' => 'eca', 'EL10Ac2g04398' => 'bvu', 'EL10Ac5g11290' => 'bvu', 'EL10Ac5g11747' => 'bvu', 'EL10Ac6g14952' => 'bvu', 'EL10Ac6g15651' => 'bvu', 'Eucgr.A01889' => 'egr', 'Eucgr.C02496' => 'egr', 'Eucgr.C02537' => 'egr', 'Eucgr.D00977' => 'egr', 'Eucgr.E04229' => 'egr', 'Eucgr.H01150' => 'egr', 'FAN02G3735' => 'fan', 'FAN14G2129' => 'fan', 'FAN15G2753' => 'fan', 'FAN24G2133' => 'fan', 'FAN27G0938' => 'fan', 'FvH4_2g26040' => 'fve', 'FvH4_3g12581' => 'fve', 'FvH4_6g43470' => 'fve', 'Glyma.02G188600' => 'gma', 'Glyma.02G230300' => 'gma', 'Glyma.06G220766' => 'gma', 'Glyma.09G086100' => 'gma', 'Glyma.09G154900' => 'gma', 'Glyma.10G087000' => 'gma', 'Glyma.12G163601' => 'gma', 'Glyma.12G195300' => 'gma', 'Glyma.13G307200' => 'gma', 'Glyma.14G197402' => 'gma', 'Glyma.16G205500' => 'gma', 'Gohir.A01G053000' => 'ghi', 'Gohir.A03G179100' => 'ghi', 'Gohir.A08G251900' => 'ghi', 'Gohir.A11G162000' => 'ghi', 'Gohir.A12G193500' => 'ghi', 'Gohir.D01G042600' => 'ghi', 'Gohir.D02G202800' => 'ghi', 'Gohir.D08G273500' => 'ghi', 'Gohir.D11G168200' => 'ghi', 'Gohir.D12G196000' => 'ghi', 'Gorai.002G053400' => 'gra', 'Gorai.004G291900' => 'gra', 'Gorai.005G227900' => 'gra', 'Gorai.007G179700' => 'gra', 'Gorai.008G210500' => 'gra', 'GSVIVG01007874001' => 'vvi', 'GSVIVG01018392001' => 'vvi', 'GSVIVG01023615001' => 'vvi', 'GSVIVG01029312001' => 'vvi', 'GSVIVG01030612001' => 'vvi', 'HanXRQChr02g0049261' => 'han', 'HanXRQChr11g0342991' => 'han', 'HanXRQChr14g0460871' => 'han', 'HanXRQChr15g0479181' => 'han', 'Haze_07055' => 'cav', 'Haze_07099' => 'cav', 'Haze_12890' => 'cav', 'Haze_19200' => 'cav', 'Hma1.2p1_0044F.1_g026350' => 'hma', 'Hma1.2p1_0074F.1_g039060' => 'hma', 'Hma1.2p1_0249F.1_g102410' => 'hma', 'Hma1.2p1_0413F.1_g147450' => 'hma', 'Hma1.2p1_0452F.1_g156000' => 'hma', 'Hma1.2p1_1340F.1_g276810' => 'hma', 'Hma1.2p1_2032F.1_g311840' => 'hma', 'HPP92_002520' => 'vpl', 'HPP92_002521' => 'vpl', 'HPP92_003016' => 'vpl', 'HPP92_003170' => 'vpl', 'HPP92_004137' => 'vpl', 'HPP92_018583' => 'vpl', 'HPP92_027539' => 'vpl', 'HPP92_028245' => 'vpl', 'Hund06539' => 'sun', 'Hund10041' => 'sun', 'Hund16383' => 'sun', 'Lalb_Chr01g0008741' => 'lal', 'Lalb_Chr04g0252071' => 'lal', 'Lalb_Chr08g0234191' => 'lal', 'Lalb_Chr14g0375771' => 'lal', 'Lalb_Chr17g0341011' => 'lal', 'Lalb_Chr22g0349581' => 'lal', 'Lj1g0017595' => 'lja', 'Lj2A254G96' => 'lonja', 'Lj2A897G22' => 'lonja', 'Lj2A916G17' => 'lonja', 'Lj2C1193G4' => 'lonja', 'Lj2C1193T5' => 'lonja', 'Lj2g0007036' => 'lja', 'Lj2g0026755' => 'lja', 'Lj3g0003760' => 'lja', 'Lj3g0023725' => 'lja', 'Lj6g0019922' => 'lja', 'Lj8C296G8' => 'lonja', 'Lj9A717G70' => 'lonja', 'LjContig00141g0005615' => 'lja', 'LjContig00408g0012312' => 'lja', 'Lsat_1_v5_gn_1_77441' => 'lsa', 'Lsat_1_v5_gn_2_115520' => 'lsa', 'Lsat_1_v5_gn_3_43740' => 'lsa', 'Lsat_1_v5_gn_4_71881' => 'lsa', 'Manes.09G102900' => 'mes', 'Manes.10G006300' => 'mes', 'Manes.12G122900' => 'mes', 'Manes.13G102900' => 'mes', 'Manes.14G171700' => 'mes', 'Mapoly0013s0143' => 'mpo', 'MBI02_g10103_MAGBIO' => 'mbi', 'MBI07_g21925_MAGBIO' => 'mbi', 'MBI07_g35970_MAGBIO' => 'mbi', 'MBI07_g35971_MAGBIO' => 'mbi', 'MBI07_g35972_MAGBIO' => 'mbi', 'MBI07_g35973_MAGBIO' => 'mbi', 'MBI15_g37111_MAGBIO' => 'mbi', 'MD01G1026000' => 'mdo', 'MD02G1006800' => 'mdo', 'MD05G1249600' => 'mdo', 'MD07G1081600' => 'mdo', 'MD07G1081900' => 'mdo', 'MD09G1106100' => 'mdo', 'MD09G1106200' => 'mdo', 'MD10G1230000' => 'mdo', 'MD12G1177800' => 'mdo', 'MD12G1178000' => 'mdo', 'MD15G1144200' => 'mdo', 'MD15G1151800' => 'mdo', 'MD15G1152000' => 'mdo', 'MD17G1094000' => 'mdo', 'Medtr1g054885' => 'mtr', 'Medtr2g067610' => 'mtr', 'Medtr2g088390' => 'mtr', 'Medtr2g088750' => 'mtr', 'Medtr5g072520' => 'mtr', 'Medtr6g059930' => 'mtr', 'MELO3C010216.2' => 'cme', 'MELO3C015000.2' => 'cme', 'MELO3C016003.2' => 'cme', 'MELO3C019241.2' => 'cme', 'MELO3C026398.2' => 'cme', 'Migut.C00627' => 'egut', 'Migut.D00210' => 'egut', 'Migut.E00650' => 'egut', 'Migut.E01629' => 'egut', 'Migut.J01348' => 'egut', 'Migut.N00508' => 'egut', 'MSTRG.19564' => 'ama', 'MSTRG.21628' => 'ama', 'MSTRG.24300' => 'ama', 'MSTRG.4367' => 'ama', 'Nitab4.5_0000110g0490' => 'nta', 'Nitab4.5_0001714g0150' => 'nta', 'Nitab4.5_0001977g0020' => 'nta', 'Nitab4.5_0002579g0070' => 'nta', 'Nitab4.5_0003246g0050' => 'nta', 'Nitab4.5_0009049g0010' => 'nta', 'Nitab4.5_0009459g0040' => 'nta', 'Nitab4.5_0009882g0020' => 'nta', 'Nitab4.5_0011835g0010' => 'nta', 'Nn3g16277' => 'nnu', 'Nn3g18531' => 'nnu', 'Nn4g25811' => 'nnu', 'Nn8g41014' => 'nnu', 'Oeu010676.1' => 'oeu', 'Oeu019063.1' => 'oeu', 'Oeu028994.1' => 'oeu', 'Oeu031211.1' => 'oeu', 'Oeu048341.1' => 'oeu', 'Oeu050490.1' => 'oeu', 'Oeu052642.1' => 'oeu', 'Os02g0732900' => 'osa', 'Os04g0615500' => 'osa', 'Os04g0628000' => 'osa', 'Os07g0600300' => 'osa', 'Peaxi162Scf00057g00428' => 'pax', 'Peaxi162Scf00290g00510' => 'pax', 'Peaxi162Scf00401g00618' => 'pax', 'Peaxi162Scf00401g00622' => 'pax', 'Peaxi162Scf00620g00099' => 'pax', 'PGR004G1696' => 'pgr', 'PGR042G1443' => 'pgr', 'PGR102G1370' => 'pgr', 'PGR119G2470' => 'pgr', 'PGR142G3758' => 'pgr', 'PGSC0003DMG400002663' => 'stu', 'PGSC0003DMG400005164' => 'stu', 'PGSC0003DMG400011182' => 'stu', 'PGSC0003DMG400022740' => 'stu', 'PGSC0003DMG401023369' => 'stu', 'Phvul.001G015500' => 'pvu', 'Phvul.003G049700' => 'pvu', 'Phvul.004G128500' => 'pvu', 'Phvul.005G114000' => 'pvu', 'Phvul.007G265200' => 'pvu', 'Potri.006G183900' => 'ptr', 'Potri.015G106200' => 'ptr', 'Potri.016G001400' => 'ptr', 'Potri.017G037200' => 'ptr', 'Potri.018G106400' => 'ptr', 'Pp3c1_33440' => 'ppa', 'Prupe.1G162900' => 'ppe', 'Prupe.3G219400' => 'ppe', 'Prupe.4G114500' => 'ppe', 'Prupe.7G037300' => 'ppe', 'Prupe.7G263600' => 'ppe', 'Prupe.8G006000' => 'ppe', 'Psat1g111840' => 'psa', 'Psat2g055080' => 'psa', 'Psat2g121120' => 'psa', 'Psat5g263840' => 'psa', 'Psat6g086880' => 'psa', 'Psat6g086920' => 'psa', 'Psat6g210480' => 'psa', 'Psat6g210520' => 'psa', 'PSO063G7340' => 'pso', 'PSO541G0613' => 'pso', 'PSO675G6103' => 'pso', 'PSO782G4792' => 'pso', 'QL02p093345' => 'qlo', 'QL05p066249' => 'qlo', 'QL05p083180' => 'qlo', 'QL06p027864' => 'qlo', 'QL08p033683' => 'qlo', 'QL12p027581' => 'qlo', 'RcHm_v2.0_Chr2g0159941' => 'rch', 'RcHm_v2.0_Chr5g0020541' => 'rch', 'RcHm_v2.0_Chr5g0074711' => 'rch', 'RcHm_v2.0_Chr6g0294401' => 'rch', 'Rhsim01G0089700' => 'rsi', 'Rhsim06G0159000' => 'rsi', 'Rhsim07G0168000' => 'rsi', 'Rhsim12G0180800' => 'rsi', 'Sabra06G0139700' => 'sbr', 'Sabra07G0099200' => 'sbr', 'Sabra15G0126300' => 'sbr', 'Sabra16G0007400' => 'sbr', 'Sabra17G0024300' => 'sbr', 'Sabra18G0090600' => 'sbr', 'SalBow3G4054' => 'sbo', 'SalBow4G2741' => 'sbo', 'SalBow6G1134' => 'sbo', 'SalBow7G2710' => 'sbo', 'Sc09g0009330' => 'sci', 'Sc12g0008430' => 'sci', 'Sc21g0001620' => 'sci', 'Sed0000621' => 'sed', 'Sed0004324' => 'sed', 'Sed0004576' => 'sed', 'Sed0015912' => 'sed', 'Sed0018966' => 'sed', 'Sed0019974' => 'sed', 'Sed0023532' => 'sed', 'SEGI_02601' => 'sgi', 'SEGI_14060' => 'sgi', 'SEGI_20416' => 'sgi', 'SGA_v2.0_scaffold15G07491' => 'sas', 'SGA_v2.0_scaffold1G00373' => 'sas', 'SGA_v2.0_scaffold326G48703' => 'sas', 'SGA_v2.0_scaffold374G50225' => 'sas', 'SGA_v2.0_scaffold45G17032' => 'sas', 'SGA_v2.0_scaffold4792G54536' => 'sas', 'SMO351G0237' => 'smo', 'SMO356G0178' => 'smo', 'Solyc04g080060.3' => 'sly', 'Solyc04g080110.4' => 'sly', 'Solyc05g024180.3' => 'sly', 'Solyc07g005570.4' => 'sly', 'Solyc08g080250.4' => 'sly', 'Solyc09g009400.4' => 'sly', 'Sopen04g033650' => 'spe', 'Sopen05g034020' => 'spe', 'Sopen07g001670' => 'spe', 'Sopen08g028600' => 'spe', 'Sopen09g004140' => 'spe', 'Sp2g25120' => 'spa', 'Sp3g19740' => 'spa', 'Sp3g21710' => 'spa', 'Sp6g19600' => 'spa', 'TAR362G0683' => 'tar', 'TAR383G0609' => 'tar', 'TAR383G0766' => 'tar', 'TAR622G1420' => 'tar', 'TAR626G0771' => 'tar', 'TAR626G0942' => 'tar', 'TAR626G1312' => 'tar', 'TAR627G0835' => 'tar', 'TAR636G3379' => 'tar', 'THA.LOC104799657' => 'tha', 'THA.LOC104801782' => 'tha', 'THA.LOC104808496' => 'tha', 'THA.LOC104811834' => 'tha', 'THA.LOC104821652' => 'tha', 'THA.LOC104821753' => 'tha', 'Thecc.02G124300' => 'tca', 'Thecc.03G140200' => 'tca', 'Thecc.04G120300' => 'tca', 'Thecc.07G119500' => 'tca', 'Thecc.09G029300' => 'tca', 'Thhalv10002534m.g' => 'esa', 'Thhalv10004339m.g' => 'esa', 'Thhalv10013543m.g' => 'esa', 'Thhalv10021082m.g' => 'esa', 'TPR.G21238' => 'tpr', 'TPR.G21243' => 'tpr', 'TPR.G22151' => 'tpr', 'TPR.G27010' => 'tpr', 'TPR.G34742' => 'tpr', 'TPR.G4213' => 'tpr', 'TPR.G5787' => 'tpr', 'TWI14G1147' => 'twi', 'TWI63G1093' => 'twi', 'TWI75G0027' => 'twi', 'unitig_22.g6781' => 'ugi', 'unitig_61.g26306' => 'ugi', 'unitig_736.g22289' => 'ugi', 'unitig_749.g13840' => 'ugi', 'vmacro06079' => 'vma', 'vmacro12225' => 'vma', 'vmacro16754' => 'vma', 'vmacro20681' => 'vma', 'VMungo0251G1289' => 'vmu', 'VMungo0464G1624' => 'vmu', 'VMungo0647G2236' => 'vmu', 'VMungo0720G2900' => 'vmu', 'VMungo1080G0041' => 'vmu', 'Zm00001eb070770' => 'zma', 'Zm00001eb071730' => 'zma', 'Zm00001eb190190' => 'zma', 'Zm00001eb244100' => 'zma' ) $gf_id = 'HOM05D001198' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001198' ) $data_identifier = 'HOM05D001198' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 8, 'amhyb' => (int) 3, 'aly' => (int) 4, 'aox' => (int) 7, 'arhy' => (int) 18, 'ath' => (int) 4, 'atr' => (int) 4, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 10, 'bol' => (int) 5, 'bra' => (int) 6, 'can' => (int) 4, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 5, 'ccl' => (int) 5, 'cil' => (int) 6, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 6, 'csa' => (int) 5, 'camsi' => (int) 6, 'dca' => (int) 5, 'din' => (int) 8, 'dzi' => (int) 4, 'eca' => (int) 3, 'bvu' => (int) 5, 'egr' => (int) 6, 'fan' => (int) 5, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 5, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 7, 'vpl' => (int) 8, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 8, 'lonja' => (int) 7, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 7, 'mdo' => (int) 14, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 4, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 5, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 1, 'ppe' => (int) 6, 'psa' => (int) 8, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 4, 'sci' => (int) 3, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 6, 'smo' => (int) 2, 'sly' => (int) 6, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 5, 'esa' => (int) 4, 'tpr' => (int) 7, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 4, 'vmu' => (int) 5, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb244100' $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